Experiment set8IT034 for Pseudomonas fluorescens FW300-N2E2

4-Hydroxybenzoic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 4-Hydroxybenzoic Acid (5 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
Growth: about 2.6 generations
By: Mark on 1/21/2016
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 10 genes in this experiment

For carbon source 4-Hydroxybenzoic Acid in Pseudomonas fluorescens FW300-N2E2

For carbon source 4-Hydroxybenzoic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Protocatechuate branch of beta-ketoadipate pathway	6
Catechol branch of beta-ketoadipate pathway	1
Chloroaromatic degradation pathway	1
p-Hydroxybenzoate degradation	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via hydroxylation
• 2,4-Dichlorobenzoate degradation
• Styrene degradation
• Butanoate metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
protocatechuate degradation II (ortho-cleavage pathway)	4	4	3
3-oxoadipate degradation	2	2	1
toluene degradation III (aerobic) (via p-cresol)	11	8	5
aromatic compounds degradation via β-ketoadipate	9	7	4
catechol degradation III (ortho-cleavage pathway)	6	4	2
superpathway of salicylate degradation	7	4	2
4-methylcatechol degradation (ortho cleavage)	7	3	2
4-chlorobenzoate degradation	4	2	1
4-methylphenol degradation to protocatechuate	4	2	1
4-sulfocatechol degradation	4	2	1
catechol degradation to β-ketoadipate	4	2	1
adipate degradation	5	5	1
4-coumarate degradation (aerobic)	5	2	1
bisphenol A degradation	5	2	1
fatty acid salvage	6	6	1
superpathway of aerobic toluene degradation	30	14	5
4-hydroxymandelate degradation	6	2	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	15	5
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
spongiadioxin C biosynthesis	7	2	1
polybrominated dihydroxylated diphenyl ethers biosynthesis	8	2	1
mandelate degradation to acetyl-CoA	18	9	2
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
oleate β-oxidation	35	30	3
2-methyl-branched fatty acid β-oxidation	14	11	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	10	1